How to know a RNA-seq is polyA or total-RNA-seq in GEO?
Does GEO require that kind of meta data during submission?
Thanks,
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bxia
1 answer
As a rule of thumb, if a project doesn't explicitly mention looking at total RNA then the odds are high that it's polyA selected. When in doubt, you can always align against rRNA, since the alignment rate for polyA selected samples will be very low (<<1%), while rRNA-depleted (aka "total RNA") will have >1% rRNA (sometimes up to ~30%).
That or trying to discern from the methods what they did.
Note that even alignment is not guaranteed to distinguish the two. Our core has sequenced plenty of polyA-selected libraries that contain substantial amounts of rRNA (some people are better at library prep than others).
Wow, I haven't seen any polyA samples over 0.1% or so rRNA come through our core. Of course I've seen rRNA-depleted samples with 30-40% rRNA, so perhaps we're trading off high polyA quality for low rRNA quality :P
Our core takes a laissez-faire approach to library prep - we offer as much guidance as the user is willing to accept, but ultimately it's the user's responsibility to make good libraries (or not). If the libraries pass basic QC (PicoGreen quantification, plus Bioanalyzer for adapter dimers), they get sequenced. We've had a few that were >90% rRNA/multi-mappers (essentially total RNA).
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